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PODCAST

Base by Base

Base by Base explores advances in genetics and genomics, with a focus on gene-disease associations, variant interpretation, protein structure, and insights from exome and genome sequencing. Each episode breaks down key studies and their clinical relevance—one base at a time. Powered by AI, Base by Base offers a new way to learn on the go. Special thanks to authors who publish under CC BY 4.0, making open-access science faster to share and easier to explore.

science life sciences

All Episodes

00:13:22

️ 76: Whole-genome Ancestry of an Old Kingdom Egyptian

Base by Base ·

2025/07/15

️ Episode 76: Whole-genome Ancestry of an Old Kingdom Egyptian In this episode of PaperCast Base by Base, we explore the first 2× coverage whole-genome sequence recovered from a high-status individual of the Old Kingdom excavated at the Nuwayrat necropolis and examine the evidence for multi-regional ancestry during early Dynastic Egypt. Study Highlights:The research team extracted and authenticated ancient DNA from a pot-burial dating to 2855–2570 cal BCE

en-us

00:13:21

🎙️ 76: Whole-genome Ancestry of an Old Kingdom Egyptian

Base by Base ·

2025/07/15

🎙️ Episode 76: Whole-genome Ancestry of an Old Kingdom Egyptian🧬 In this episode of PaperCast Base by Base, we explore the first 2× coverage whole-genome sequence recovered from a high-status individual of the Old Kingdom excavated at the Nuwayrat necropolis and examine the evidence for multi-regional ancestry during early Dynastic Egypt.🔍 Study Highlights:The research team extracted and authenticated ancient DNA from a pot-burial dating to 2855–2570 cal BCE and generated a 2.02× coverage genome

en-us

00:14:55

🎙️ 75: Metabolic Shaping of Enzyme Structures Over...

Base by Base ·

2025/07/14

🎙️ Episode 75: Metabolic Shaping of Enzyme Structures Over 400 Million Years🧬 In this episode of PaperCast Base by Base, we explore a large-scale study published in Nature by Lemke et al. that leverages AlphaFold2-predicted and experimentally determined enzyme structures across 27 yeast species to reveal how metabolic properties have constrained and shaped enzyme structural evolution over 400 million years in the Saccharomycotina subphylum.🔍 Study Highlights:The authors analyzed over 11,000

en-us

00:14:56

️ 75: Metabolic Shaping of Enzyme Structures Over 400...

Base by Base ·

2025/07/14

️ Episode 75: Metabolic Shaping of Enzyme Structures Over 400 Million Years In this episode of PaperCast Base by Base, we explore a large-scale study published in Nature by Lemke et al. that leverages AlphaFold2-predicted and experimentally determined enzyme structures across 27 yeast species to reveal how metabolic properties have constrained and shaped enzyme structural evolution over 400 million years in the Saccharomycotina subphylum. Study

en-us

00:20:10

️ 74: Benchmarking T Cell Receptor–Epitope Predictors...

Base by Base ·

2025/07/13

️ Episode 74: Benchmarking T Cell Receptor–Epitope Predictors with ePytope-TCR In this episode of PaperCast Base by Base, we explore a unified computational framework that integrates and benchmarks 21 T cell receptor–epitope binding prediction models to evaluate their performance on viral epitope repertoires and deep mutational scans. Study Highlights:The authors developed ePytope-TCR, which standardizes 18 general and three categorical prediction methods

en-us

00:20:09

🎙️ 74: Benchmarking T Cell Receptor–Epitope...

Base by Base ·

2025/07/13

🎙️ Episode 74: Benchmarking T Cell Receptor–Epitope Predictors with ePytope-TCR🧬 In this episode of PaperCast Base by Base, we explore a unified computational framework that integrates and benchmarks 21 T cell receptor–epitope binding prediction models to evaluate their performance on viral epitope repertoires and deep mutational scans.🔍 Study Highlights:The authors developed ePytope-TCR, which standardizes 18 general and three categorical prediction methods into a single interoperable platform

en-us

00:15:54

🎙️ 73: Assessing Family History in Dementia Genetics:...

Base by Base ·

2025/07/12

🎙️ Episode 73: Assessing Family History in Dementia Genetics: Enhancing Diagnostic Yield🧬 In this episode of PaperCast Base by Base, we explore a study that evaluates how stratifying dementia patients by family history and age at onset can optimize the identification of diagnostically significant genetic variants in a clinical memory clinic setting, illustrating gene–disease association and variant interpretation through exome sequencing discoveries in neurodegenerative disease.🔍 Study

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00:15:55

️ 73: Assessing Family History in Dementia Genetics:...

Base by Base ·

2025/07/12

️ Episode 73: Assessing Family History in Dementia Genetics: Enhancing Diagnostic Yield In this episode of PaperCast Base by Base, we explore a study that evaluates how stratifying dementia patients by family history and age at onset can optimize the identification of diagnostically significant genetic variants in a clinical memory clinic setting, illustrating gene–disease association and variant interpretation through exome sequencing discoveries in

en-us

00:19:43

🎙️ 72: The POC5 Syndrome — A Ciliopathy Linking...

Base by Base ·

2025/07/11

🎙️ Episode 72: The POC5 Syndrome — A Ciliopathy Linking Retina, Muscles and Metabolism🧬 In this episode of Base by Base, we explore a multi-institutional study by Vulto-van Silfhout et al. (2025), published in Genetics in Medicine, that uncovers a novel syndromic ciliopathy caused by bi-allelic loss-of-function variants in the POC5 gene. The research describes twelve families with a rare constellation of clinical features—including rod-cone dystrophy, severe insulin-resistant diabetes, partial

en-us

00:19:44

️ 72: The POC5 Syndrome — A Ciliopathy Linking...

Base by Base ·

2025/07/11

️ Episode 72: The POC5 Syndrome — A Ciliopathy Linking Retina, Muscles and Metabolism In this episode of Base by Base, we explore a multi-institutional study by Vulto-van Silfhout et al. (2025), published in Genetics in Medicine, that uncovers a novel syndromic ciliopathy caused by bi-allelic loss-of-function variants in the POC5 gene. The research describes twelve families with a rare constellation of clinical features—including rod-cone dystrophy,

en-us

00:25:15

🎙️ 71: ELFN1 Deficiency Disorder — Mechanistic Basis...

Base by Base ·

2025/07/10

🎙️ Episode 71: ELFN1 Deficiency Disorder — Mechanistic Basis and Phenotypic Spectrum of a Neurodevelopmental Disorder with Epilepsy🧬 In this episode of Base by Base, we dive into the recent pre-proof study by Dore et al. (2025) in Genetics in Medicine, which defines a new autosomal recessive neurodevelopmental syndrome caused by biallelic variants in the synaptic adhesion molecule ELFN1. Through detailed clinical phenotyping of fourteen patients, molecular assays in human cells, and in vivo

en-us

00:25:16

️ 71: ELFN1 Deficiency Disorder — Mechanistic Basis...

Base by Base ·

2025/07/10

️ Episode 71: ELFN1 Deficiency Disorder — Mechanistic Basis and Phenotypic Spectrum of a Neurodevelopmental Disorder with Epilepsy In this episode of Base by Base, we dive into the recent pre-proof study by Dore et al. (2025) in Genetics in Medicine, which defines a new autosomal recessive neurodevelopmental syndrome caused by biallelic variants in the synaptic adhesion molecule ELFN1. Through detailed clinical phenotyping of fourteen patients, molecular

en-us

00:19:09

🎙️ 70: Scalable Screening of Ternary-Code DNA...

Base by Base ·

2025/07/09

🎙️ Episode 70: Scalable Screening of Ternary-Code DNA Methylation Dynamics Associated with Human Traits🧬 In this episode of Base por Base, we delve into a methodological breakthrough reported by Goldberg et al. (2025) in Cell Genomics, where the authors introduce the methylation screening array (MSA) — a next-generation Infinium BeadChip designed for large-scale, high-throughput profiling of DNA cytosine modifications across human populations. By integrating curated trait-associated loci from

en-us

00:19:10

️ 70: Scalable Screening of Ternary-Code DNA...

Base by Base ·

2025/07/09

️ Episode 70: Scalable Screening of Ternary-Code DNA Methylation Dynamics Associated with Human Traits In this episode of Base por Base, we delve into a methodological breakthrough reported by Goldberg et al. (2025) in Cell Genomics, where the authors introduce the methylation screening array (MSA) — a next-generation Infinium BeadChip designed for large-scale, high-throughput profiling of DNA cytosine modifications across human populations. By

en-us

00:16:15

️ 69: Synthetic Dosage Lethality of PLK1 — Targetable...

Base by Base ·

2025/07/08

️ Episode 69: Synthetic Dosage Lethality of PLK1 — Targetable Vulnerabilities in PLK1-Overexpressing Cancers In this episode of Base por Base, we delve into a comprehensive study by Cunningham et al. (2025) in Cell Genomics that harnesses genome-wide synthetic dosage lethality (SDL) screening to uncover novel therapeutic targets in cancers driven by Polo-like kinase 1 (PLK1). By integrating pooled shRNA and CRISPR-Cas9 screens in both in vitro and in vivo

en-us

00:16:14

🎙️ 69: Synthetic Dosage Lethality of PLK1 —...

Base by Base ·

2025/07/08

🎙️ Episode 69: Synthetic Dosage Lethality of PLK1 — Targetable Vulnerabilities in PLK1-Overexpressing Cancers🧬 In this episode of Base por Base, we delve into a comprehensive study by Cunningham et al. (2025) in Cell Genomics that harnesses genome-wide synthetic dosage lethality (SDL) screening to uncover novel therapeutic targets in cancers driven by Polo-like kinase 1 (PLK1). By integrating pooled shRNA and CRISPR-Cas9 screens in both in vitro and in vivo patient-derived xenograft models,

en-us

00:16:04

️ 68: Indels Empower Antiviral Proteins to Achieve...

Base by Base ·

2025/07/07

️ Episode 68: Indels Empower Antiviral Proteins to Achieve Functional Novelty Beyond Missense Mutations In this episode of Base by Base, we dive into pioneering work by Tenthorey et al. (2025) in Cell Genomics that uncovers how insertion and deletion mutations—indels—can unlock evolutionary innovations in the antiviral protein TRIM5α. By applying both deep mutational scanning and a novel deep indel scanning approach to the v1 loop of human TRIM5α, the

en-us

00:16:03

🎙️ 68: Indels Empower Antiviral Proteins to Achieve...

Base by Base ·

2025/07/07

🎙️ Episode 68: Indels Empower Antiviral Proteins to Achieve Functional Novelty Beyond Missense Mutations🧬 In this episode of Base by Base, we dive into pioneering work by Tenthorey et al. (2025) in Cell Genomics that uncovers how insertion and deletion mutations—indels—can unlock evolutionary innovations in the antiviral protein TRIM5α. By applying both deep mutational scanning and a novel deep indel scanning approach to the v1 loop of human TRIM5α, the authors reveal that while no

en-us

00:14:46

🎙️ 67: Smarter Signals — How Multimodal AI Boosts...

Base by Base ·

2025/07/06

🎙️ Episode 67: Smarter Signals — How Multimodal AI Boosts Genetic Prediction of Heart Disease🧬 In this episode of Base por Base, we delve into a major advancement in the intersection of artificial intelligence and cardiovascular genomics. A study by Zhou et al. (2025), published in The American Journal of Human Genetics, introduces M-REGLE (Multimodal Representation Learning for Genetic Discovery on Low-dimensional Embeddings), a novel AI framework designed to enhance genome-wide association

en-us

00:14:47

️ 67: Smarter Signals — How Multimodal AI Boosts...

Base by Base ·

2025/07/06

️ Episode 67: Smarter Signals — How Multimodal AI Boosts Genetic Prediction of Heart Disease In this episode of Base por Base, we delve into a major advancement in the intersection of artificial intelligence and cardiovascular genomics. A study by Zhou et al. (2025), published in The American Journal of Human Genetics, introduces M-REGLE (Multimodal Representation Learning for Genetic Discovery on Low-dimensional Embeddings), a novel AI framework designed

en-us

452 results

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